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Gramicidin D complex with sodium iodide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1W5U PDB ENTRY 1W5U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH CRYSTALLIZATION WITH 30 MG/ML GRAMICIDIN AND SATURATED NAI IN METHANOL
Crystal Properties Matthews coefficient Solvent content 1.61 23.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 29.816 α = 90 b = 31.255 β = 90 c = 51.667 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MAR CCD 165 mm 2000-10-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 5ID-B APS 5ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.25 26.74 19883 2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R PDB ENTRY 1W5U 1.25 26.74 24628 100 0.164 0.1653 0.1756 RANDOM
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3]
Coordinate Error Structure Solution Method Refinement High Resolution Refinement Low Resolution 26 556.13 566.51
RMS Deviations Key Refinement Restraint Deviation s_zero_chiral_vol 0.146 s_non_zero_chiral_vol 0.126 s_similar_adp_cmpnt 0.041 s_angle_d 0.035 s_from_restr_planes 0.033 s_bond_d 0.015 s_rigid_bond_adp_cmpnt 0.006 s_similar_dist s_anti_bump_dis_restr s_approx_iso_adps
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 566 Nucleic Acid Atoms Solvent Atoms 42 Heterogen Atoms 17
Software Software Software Name Purpose AMoRE phasing SHELXL-97 refinement DENZO data reduction SCALEPACK data scaling